refactor(manifest): split Manifest into ManifestIndex + Manifest single-value type

Manifest now holds exactly one agent and one effective bottle (with
git_user overlay already applied). The old multi-agent/bottle
collection is renamed ManifestIndex. BottleSpec.manifest starts as
ManifestIndex from the CLI and becomes Manifest after _validate()
calls load_for_agent(); all provisioning code downstream reads
spec.manifest.agent / spec.manifest.bottle instead of indexing by name.

tests/unit/test_smolmachines_provision.py

@@ -33,7 +33,7 @@ from bot_bottle.backend.smolmachines.launch import _bundle_launch_spec
 from bot_bottle.backend.util import AGENT_CA_PATH
 from bot_bottle.egress import EgressPlan, EgressRoute
 from bot_bottle.git_gate import GitGatePlan, GitGateUpstream
-from bot_bottle.manifest import ManifestGitEntry, ManifestKeyConfig, Manifest
+from bot_bottle.manifest import ManifestGitEntry, ManifestKeyConfig, Manifest, ManifestIndex
 from bot_bottle.supervise import SupervisePlan
 
 
@@ -110,7 +110,7 @@ def _plan(
         bottle_json["git-gate"] = git_gate_json
     if supervise:
         bottle_json["supervise"] = True
-    manifest = Manifest.from_json_obj({
+    manifest = ManifestIndex.from_json_obj({
         "bottles": {"dev": bottle_json},
         "agents": {
             "demo": {
@@ -119,7 +119,7 @@ def _plan(
                 "bottle": "dev",
             },
         },
-    })
+    }).load_for_agent("demo")
     spec = BottleSpec(
         manifest=manifest,
         agent_name="demo",